Delays in construction work - coupled with over-optimistic estimates - has left Labour's flagship education reforms behind schedule, it is disclosed.

The National Audit Office also said a further £1.9bn of taxpayers' money that should have been spent on books, computers and teachers' salaries is also languishing in school accounts.

Ministers have already threatened to claw back cash from schools after it emerged around 20,500 out of 22,500 primaries and secondaries in England had an average surplus of £99,500 each.

The money could be given back to councils to spend boosting standards among deprived pupils, ministers said.

But David Laws, the Liberal Democrat children's spokesman, said it was "not surprising" schools were hoarding cash and insisted the "massive underspend" on buildings made a mockery of Gordon Brown's financial stimulus. It followed his claim that thousands of new jobs would be created reconstructing schools and hospitals.

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"Given this Government's tendency towards boom-bust financing of public services, it is not surprising that so many schools have felt the need to build up surpluses," he said. "Instead of attempting to claw this money back, ministers need to get a grip on school funding so it is allocated fairly."

The so-called Building Schools for the Future programme aims to rebuild or refurbish every secondary school in England.

Today's NAO report found the underspend on the project had increased from £1.9 billion at the end of March 2008 to around £2.4 billion in March 2009.

The NAO warned that the BSF programme will now have to be carefully managed in the future, especially in the current recession.

It said: "The Department will need to ensure that its long-term capital expenditure plans remain realistic given the difficulties private sector partners may find in securing funding in the current economic climate."